Only run downstreamViz on param

astrocyte_pkg.yml

@@ -159,6 +159,17 @@ workflow_parameters:
     description: |
       10x cellranger version.
 
+  - id: vizFiles
+    type: select
+    choices:
+      - [ 'true', 'Yes' ]
+      - [ 'false', 'No' ]
+    default: 'true'
+    required: true
+    description: |
+      Create objects which can be used for downstream visualization and analysis of each sample outputs. Currently created: Seurat R-objects.
+
+
   - id: astrocyte
     type: select
     choices:

workflow/main.nf

@@ -81,6 +81,7 @@ expectCells = params.expectCells
 forceCells = params.forceCells
 chemistryParam = params.chemistryParam
 version = params.version
+vizFiles = params.vizFiles
 outDir = params.outDir
 
 // Define script files
@@ -397,6 +398,9 @@ process downstreamViz {
     file "*.rds" into seuratPaths
     file "version_seurat.txt" into version_seurat
 
+  when:
+    vizFiles
+
   script:
     """
     hostname